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NOAA's Deep-ocean Assessment and Reporting of Tsunamis (DART) data are critical for NASA-JPL's tsunami detection, real-time operations, and oceanographic research. However, these time-series data often contain spikes, steps, and drifts that degrade data quality and obscure essential oceanographic features. To address these anomalies, the work introduces an Iterative Encoding-Decoding Variational Autoencoders (Iterative Encoding-Decoding VAEs) model to improve the quality of DART time series. Unlike traditional filtering and thresholding methods that risk distorting inherent signal characteristics, Iterative Encoding-Decoding VAEs progressively remove anomalies while preserving the data's latent structure. A hybrid thresholding approach further retains genuine oceanographic features near boundaries. Applied to complex DART datasets, this approach yields reconstructions that better maintain key oceanic properties compared to classical statistical techniques, offering improved robustness against spike removal and subtle step changes. The resulting high-quality data supports critical verification and validation efforts for the GRACE-FO mission at NASA-JPL, where accurate surface measurements are essential to modeling Earth's gravitational field and global water dynamics. Ultimately, this data processing method enhances tsunami detection and underpins future climate modeling with improved interpretability and reliability.